SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects.

The composition of the gut microbiota is a known factor in various diseases and has proven to be a strong basis for automatic classification of disease state. A need for a better understanding of microbiota data on the functional scale has since been voiced, as it would enhance these approaches' biological interpretability. In this paper, we have developed a computational pipeline for integrating the functional annotation of the gut microbiota into an automatic classification process and facilitating downstream interpretation of its results.

Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples.

Aim: The current study investigated the performance of 4 widely used DNA extraction kits using different types of high (stool) and low biomass samples (chyme, broncho alveolar lavage and sputum).

Methods: Qiagen Powerfecal Pro DNA kit, Macherey Nucleospin Soil kit, Macherey Nucleospin Tissue Kit and MagnaPure LC DNA isolation kit III were evaluated in terms of DNA quantity, quality, diversity and composition profiles.

Results: The quantity and quality of DNA varied among the four kits.

Gut microbiota analysis for prediction of clinical relapse in Crohn's disease.

The role of intestinal bacterial microbiota has been described as key in the pathophysiology of Crohn's disease (CD). CD is characterized by frequent relapses after periods of remission which are not entirely understood. In this paper, we investigate whether the heterogeneity in microbiota profiles in CD patients could be a suitable predictor for these relapses.

Different Fecal Microbiota in Hirschsprung's Patients With and Without Associated Enterocolitis.

Background And Objectives: Patients with Hirschsprung's disease are at risk of developing Hirschsprung-associated enterocolitis, especially in the first 2 years of life. The pathophysiology of this inflammatory disease remains unclear, and intestinal dysbiosis has been proposed in the last decade. The primary objective of this study was to evaluate in a large cohort if Hirschsprung-associated enterocolitis was associated with alterations of fecal bacterial composition compared with HD without enterocolitis in different age groups.

Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests.

Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies with an innovative and significant approach consisting of processing steps and quality assessment for interpreting metagenomics data used for diagnosis. Here, we propose a methodology for taxon identification and abundance assessment of shotgun sequencing data of microbes that are well fitted for clinical setup.